LAMMPS (27 Jun 2024)
# ------ 2D oxidizing bar ------ #

dimension          2
units              lj
atom_style         hybrid rheo/thermal bond
boundary           m m p
comm_modify        vel yes
newton             off

region             box block -60 60 0 80 -0.01 0.01 units box
create_box         3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
Created orthogonal box = (-60 0 -0.01) to (60 80 0.01)
  2 by 2 by 1 MPI processor grid

region             lbar block -15 0 3 80 EDGE EDGE units box
region             rbar block 0 15 3 80 EDGE EDGE units box
region             bar union 2 lbar rbar
region             floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box

lattice            hex 1.0
Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699
create_atoms       1 region bar
Created 2255 atoms
  using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
  create_atoms CPU = 0.004 seconds
create_atoms       3 region floor
Created 446 atoms
  using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01)
  create_atoms CPU = 0.000 seconds

set                region rbar type 2
Setting atom values ...
  1148 settings made for type
group              bar type 1 2
2255 atoms in group bar
group              rbar type 2
1148 atoms in group rbar
group              floor type 3
446 atoms in group floor

set                group all sph/e 0.0
Setting atom values ...
  2701 settings made for sph/e
set                group all rheo/status 1
Setting atom values ...
  2701 settings made for rheo/status

# ------ Model parameters ------#

variable           cut equal 3.0
variable           n equal 1.0
variable           rho0 equal 1.0
variable           cs equal 1.0
variable           mp equal ${rho0}/${n}
variable           mp equal 1/${n}
variable           mp equal 1/1
variable           zeta equal 0.05
variable           kappa equal 0.1*${rho0}/${mp}
variable           kappa equal 0.1*1/${mp}
variable           kappa equal 0.1*1/1
variable           dt_max equal 0.1*${cut}/${cs}/3
variable           dt_max equal 0.1*3/${cs}/3
variable           dt_max equal 0.1*3/1/3
variable           eta equal 0.05
variable           Cv equal 1.0
variable           L equal 0.1
variable           Tf equal 1.0

mass               * ${mp}
mass               * 1
timestep           0.1

pair_style         hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid
pair_style         hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid
pair_style         hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid
pair_coeff         * * rheo
pair_coeff         * * rheo/solid 1.0 1.0 1.0

special_bonds      lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     0 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.000 seconds
create_bonds       many bar bar 1 0 1.5
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 73 49 1
  3 neighbor lists, perpetual/occasional/extra = 2 1 0
  (1) command create_bonds, occasional
      attributes: full, newton off
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (2) pair rheo, perpetual
      attributes: half, newton off
      pair build: half/bin/newtoff
      stencil: full/bin/2d
      bin: standard
  (3) pair rheo/solid, perpetual, trim from (2)
      attributes: half, newton off, cut 1.3
      pair build: trim
      stencil: none
      bin: none
Added 6547 bonds, new total = 6547
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     6 = max # of 1-2 neighbors
   101 = max # of special neighbors
  special bonds CPU = 0.000 seconds
special_bonds      lj 0.0 1.0 1.0 coul 1.0 1.0 1.0

bond_style         hybrid bpm/spring rheo/shell t/form 100
bond_coeff         1 bpm/spring 1.0 1.0 1.0
bond_coeff         2 rheo/shell 0.2 0.2 0.1

# ------ Apply dynamics ------#

# Note: surface detection is not performed on solid bodies, so cannot use surface property
compute         coord all rheo/property/atom coordination
variable        surf atom c_coord<22
group           surf dynamic all var surf every 10
dynamic group surf defined

fix             1 all rheo ${cut} quintic 0                            thermal                            shift                            surface/detection coordination 22 8
fix             1 all rheo 3 quintic 0                            thermal                            shift                            surface/detection coordination 22 8
fix             2 all rheo/viscosity * constant ${eta}
fix             2 all rheo/viscosity * constant 0.05
fix             3 all rheo/pressure * linear
fix             4 all rheo/thermal conductivity * constant ${kappa}                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant ${Cv}                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant ${Tf}                                    latent/heat * constant ${L}                                    react 1.5 1
fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant ${L}                                    react 1.5 1
fix             4 all rheo/thermal conductivity * constant 0.1                                    specific/heat * constant 1                                    Tfreeze * constant 1                                    latent/heat * constant 0.1                                    react 1.5 1

fix             5 rbar rheo/oxidation 1.5 2 1.0
fix             6 all wall/harmonic ylo EDGE 2.0 1.0 1.0
fix             7 all gravity 5e-5 vector 0 -1 0
fix             8 floor setforce 0.0 0.0 0.0
fix             9 surf add/heat linear 1.1 0.5
fix             10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
fix             11 all enforce2d

compute         surf all rheo/property/atom surface
compute         rho all rheo/property/atom rho
compute         phase all rheo/property/atom phase
compute         temp all rheo/property/atom temperature
compute         eng all rheo/property/atom energy
compute         nbond_shell all rheo/property/atom nbond/shell
compute         nbond_solid all nbond/atom bond/type 1

# ------ Output & Run ------ #

thermo          200
thermo_style    custom step time ke press atoms

#dump            1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf

run             40000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- BPM bond style: doi:10.1039/D3SM01373A

@Article{Clemmer2024,
 author =  {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.},
 title =   {A soft departure from jamming: the compaction of deformable
            granular matter under high pressures},
 journal = {Soft Matter},
 year =    2024,
 volume =  20,
 number =  8,
 pages =   {1702--1718}
}

- @article{PalermoInPrep,
 journal = {in prep},
 title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows},
 year = {2024},
 author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor},
}

- @article{ApplMathModel.130.310,
 title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum},
 journal = {Applied Mathematical Modelling},
 volume = {130},
 pages = {310-326},
 year = {2024},
 issn = {0307-904X},
 doi = {https://doi.org/10.1016/j.apm.2024.02.027},
 author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer},
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
  binsize = 1.65, bins = 73 49 1
  8 neighbor lists, perpetual/occasional/extra = 7 1 0
  (1) pair rheo, perpetual, half/full from (3)
      attributes: half, newton off
      pair build: halffull/newtoff
      stencil: none
      bin: none
  (2) pair rheo/solid, perpetual, trim from (4)
      attributes: half, newton off, cut 1.3
      pair build: trim
      stencil: none
      bin: none
  (3) compute RHEO/KERNEL, perpetual
      attributes: full, newton off
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (4) compute RHEO/GRAD, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
  (5) compute RHEO/VSHIFT, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
  (6) compute RHEO/SURFACE, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
  (7) fix rheo/thermal, occasional, trim from (4)
      attributes: half, newton off, cut 3
      pair build: trim
      stencil: none
      bin: none
  (8) fix rheo/oxidation, perpetual, trim from (3)
      attributes: full, newton off, cut 1.8
      pair build: trim
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes
   Step          Time          KinEng         Press         Atoms   
         0   0              0              0                   2701 
       200   20             4.1737457e-07  1.298459e-07        2701 
       400   40             1.6692448e-06  4.9223021e-07       2701 
       600   60             3.7115752e-06  1.0476692e-05       2701 
       800   80             4.678922e-06   0.00015017477       2701 
      1000   100            4.7534549e-06  0.00027967322       2701 
      1200   120            3.4532974e-06  0.00045908503       2701 
      1400   140            1.4159611e-06  0.00055855688       2701 
      1600   160            4.5151976e-07  0.00058351591       2701 
      1800   180            5.1656107e-07  0.00055163637       2701 
      2000   200            1.882995e-06   0.00048349046       2701 
      2200   220            3.3481991e-06  0.00037790487       2701 
      2400   240            3.8173347e-06  0.00023972848       2701 
      2600   260            3.1832818e-06  9.5696995e-05       2701 
      2800   280            1.5994934e-06 -2.7484809e-05       2701 
      3000   300            3.573403e-07  -8.56391e-05         2701 
      3200   320            1.6485893e-07 -5.6974248e-05       2701 
      3400   340            8.5665044e-07  3.473389e-06        2701 
      3600   360            2.0801421e-06  5.7938582e-05       2701 
      3800   380            3.1934959e-06  0.00016746888       2701 
      4000   400            3.2540476e-06  0.00026471904       2701 
      4200   420            2.5603544e-06  0.00037699521       2701 
      4400   440            1.4309318e-06  0.00047456272       2701 
      4600   460            6.5231009e-07  0.00050551979       2701 
      4800   480            6.9010626e-07  0.00048100816       2701 
      5000   500            1.2663499e-06  0.00042166061       2701 
      5200   520            2.0653769e-06  0.00033547376       2701 
      5400   540            2.2709253e-06  0.00023015884       2701 
      5600   560            1.7864994e-06  0.00013378564       2701 
      5800   580            9.5638493e-07  4.4666688e-05       2701 
      6000   600            3.0331342e-07 -1.884252e-06        2701 
      6200   620            3.451498e-07   8.3090163e-07       2701 
      6400   640            9.5098597e-07  4.7759688e-05       2701 
      6600   660            1.8169765e-06  0.00011801205       2701 
      6800   680            2.3723951e-06  0.00019823562       2701 
      7000   700            2.3542553e-06  0.00028873701       2701 
      7200   720            1.9132157e-06  0.00036386547       2701 
      7400   740            1.4123115e-06  0.00040731263       2701 
      7600   760            1.2422941e-06  0.00041151319       2701 
      7800   780            1.4355275e-06  0.00038364583       2701 
      8000   800            1.7835754e-06  0.00032724239       2701 
      8200   820            1.961321e-06   0.00025932051       2701 
      8400   840            1.8005786e-06  0.00018763659       2701 
      8600   860            1.4274768e-06  0.00012392727       2701 
      8800   880            1.075959e-06   8.1241673e-05       2701 
      9000   900            1.014674e-06   7.0104531e-05       2701 
      9200   920            1.3155353e-06  8.7991534e-05       2701 
      9400   940            1.815649e-06   0.00012975516       2701 
      9600   960            2.2699387e-06  0.0001861001        2701 
      9800   980            2.4916284e-06  0.00024375475       2701 
     10000   1000           2.4741893e-06  0.00029466715       2701 
     10200   1020           2.3835838e-06  0.00032733587       2701 
     10400   1040           2.3816351e-06  0.00033659466       2701 
     10600   1060           2.5177605e-06  0.00032136429       2701 
     10800   1080           2.6973866e-06  0.00028678114       2701 
     11000   1100           2.8219278e-06  0.00023889501       2701 
     11200   1120           2.794743e-06   0.00019226876       2701 
     11400   1140           2.667182e-06   0.00015100316       2701 
     11600   1160           2.5918212e-06  0.00012484649       2701 
     11800   1180           2.6802845e-06  0.00011912201       2701 
     12000   1200           2.9620111e-06  0.00013336302       2701 
     12200   1220           3.3281225e-06  0.00016262605       2701 
     12400   1240           3.6587842e-06  0.00020175308       2701 
     12600   1260           3.8696418e-06  0.00023984351       2701 
     12800   1280           3.9774608e-06  0.00026981166       2701 
     13000   1300           4.0621923e-06  0.00028706126       2701 
     13200   1320           4.2118368e-06  0.00028639136       2701 
     13400   1340           4.4229032e-06  0.00026844105       2701 
     13600   1360           4.6415059e-06  0.00023789752       2701 
     13800   1380           4.8106868e-06  0.00020524655       2701 
     14000   1400           4.9343741e-06  0.00017392428       2701 
     14200   1420           5.0835921e-06  0.00015013775       2701 
     14400   1440           5.3365604e-06  0.0001413941        2701 
     14600   1460           5.7248817e-06  0.00014521418       2701 
     14800   1480           6.2145391e-06  0.00016109563       2701 
     15000   1500           6.7347576e-06  0.00018481456       2701 
     15200   1520           7.221694e-06   0.00020956545       2701 
     15400   1540           7.6762698e-06  0.0002293694        2701 
     15600   1560           8.1313425e-06  0.00024058679       2701 
     15800   1580           8.6053324e-06  0.00024015877       2701 
     16000   1600           9.1091988e-06  0.00022927412       2701 
     16200   1620           9.6165964e-06  0.00021035982       2701 
     16400   1640           1.0093906e-05  0.00018782673       2701 
     16600   1660           1.0561165e-05  0.00016863993       2701 
     16800   1680           1.1066274e-05  0.00015693261       2701 
     17000   1700           1.1661861e-05  0.00015221008       2701 
     17200   1720           1.236148e-05   0.00015781879       2701 
     17400   1740           1.3124872e-05  0.00017008789       2701 
     17600   1760           1.3924606e-05  0.00018628888       2701 
     17800   1780           1.4733479e-05  0.0002011741        2701 
     18000   1800           1.5558838e-05  0.00021115187       2701 
     18200   1820           1.6415631e-05  0.00021314897       2701 
     18400   1840           1.7287377e-05  0.00020793654       2701 
     18600   1860           1.8202577e-05  0.00019550685       2701 
     18800   1880           1.9126239e-05  0.00018102715       2701 
     19000   1900           2.0074716e-05  0.0001684831        2701 
     19200   1920           2.1090982e-05  0.00015956926       2701 
     19400   1940           2.2180303e-05  0.00015805759       2701 
     19600   1960           2.3330404e-05  0.00016157807       2701 
     19800   1980           2.4557652e-05  0.00017047221       2701 
     20000   2000           2.5841568e-05  0.00018216972       2701 
     20200   2020           2.7188233e-05  0.00018953358       2701 
     20400   2040           2.8576958e-05  0.00019304182       2701 
     20600   2060           2.999218e-05   0.00019239757       2701 
     20800   2080           3.1437794e-05  0.00018759619       2701 
     21000   2100           3.2938831e-05  0.00017863274       2701 
     21200   2120           3.4506515e-05  0.00016911647       2701 
     21400   2140           3.6126713e-05  0.00016161126       2701 
     21600   2160           3.7812343e-05  0.0001583968        2701 
     21800   2180           3.9564996e-05  0.00016178647       2701 
     22000   2200           4.1406387e-05  0.00016872633       2701 
     22200   2220           4.3340255e-05  0.00017435061       2701 
     22400   2240           4.5333317e-05  0.00017910049       2701 
     22600   2260           4.7311785e-05  0.0001800877        2701 
     22800   2280           4.9303605e-05  0.00017728464       2701 
     23000   2300           5.1334424e-05  0.00017486007       2701 
     23200   2320           5.3402091e-05  0.00016867905       2701 
     23400   2340           5.5505853e-05  0.00016402807       2701 
     23600   2360           5.7679415e-05  0.00016343865       2701 
     23800   2380           5.9920078e-05  0.00016623374       2701 
     24000   2400           6.2239328e-05  0.00017028032       2701 
     24200   2420           6.4624902e-05  0.00017371561       2701 
     24400   2440           6.7054046e-05  0.00017565916       2701 
     24600   2460           6.9522453e-05  0.00017545566       2701 
     24800   2480           7.2079202e-05  0.00017437049       2701 
     25000   2500           7.4716585e-05  0.00017043497       2701 
     25200   2520           7.7415627e-05  0.00016579093       2701 
     25400   2540           8.0169507e-05  0.00016268419       2701 
     25600   2560           8.3001779e-05  0.00016233687       2701 
     25800   2580           8.5921287e-05  0.00016275719       2701 
     26000   2600           8.8880908e-05  0.00016425339       2701 
     26200   2620           9.1881788e-05  0.00016478504       2701 
     26400   2640           9.4969348e-05  0.00016371806       2701 
     26600   2660           9.817611e-05   0.00016339555       2701 
     26800   2680           0.00010146396  0.00015937569       2701 
     27000   2700           0.00010485972  0.0001562082        2701 
     27200   2720           0.00010837565  0.00015181198       2701 
     27400   2740           0.00011187666  0.00015162336       2701 
     27600   2760           0.00011543324  0.0001606148        2701 
     27800   2780           0.00011905739  0.00016161123       2701 
     28000   2800           0.00012280117  0.00016267347       2701 
     28200   2820           0.00012665753  0.00016393863       2701 
     28400   2840           0.00013061568  0.00016168097       2701 
     28600   2860           0.00013469542  0.00015439793       2701 
     28800   2880           0.00013889392  0.00014870639       2701 
     29000   2900           0.00014307887  0.00015020156       2701 
     29200   2920           0.00014714875  0.00015727801       2701 
     29400   2940           0.0001510796   0.00016230922       2701 
     29600   2960           0.0001551489   0.00016725059       2701 
     29800   2980           0.00015918695  0.0001556229        2701 
     30000   3000           0.00016145717  0.00015704562       2701 
     30200   3020           0.00016164704  0.00015902669       2701 
     30400   3040           0.00016250791  0.00017587854       2701 
     30600   3060           0.0001639094   0.00016958759       2701 
     30800   3080           0.00016479103  0.00016810892       2701 
     31000   3100           0.00016521873  0.00016027053       2701 
     31200   3120           0.00016540216  0.00015397865       2701 
     31400   3140           0.00016690063  0.00015955009       2701 
     31600   3160           0.00016832002  0.00015593907       2701 
     31800   3180           0.00016948949  0.00015690982       2701 
     32000   3200           0.0001700061   0.00016199222       2701 
     32200   3220           0.00017122936  0.00016220019       2701 
     32400   3240           0.00017198531  0.00015194229       2701 
     32600   3260           0.00017286097  0.00014880433       2701 
     32800   3280           0.00017395847  0.00014887179       2701 
     33000   3300           0.00017527125  0.00015338612       2701 
     33200   3320           0.00017667877  0.00014965389       2701 
     33400   3340           0.00017944144  0.00014195087       2701 
     33600   3360           0.0001807053   0.00014509998       2701 
     33800   3380           0.00018242869  0.00014683629       2701 
     34000   3400           0.00018415985  0.00014295872       2701 
     34200   3420           0.00018635902  0.00013823794       2701 
     34400   3440           0.00018885401  0.00013629126       2701 
     34600   3460           0.00019106836  0.000138816         2701 
     34800   3480           0.00019256787  0.00014358744       2701 
     35000   3500           0.00019410016  0.0001420669        2701 
     35200   3520           0.00019563657  0.0001340349        2701 
     35400   3540           0.00019734994  0.00012994197       2701 
     35600   3560           0.00019880477  0.00013331695       2701 
     35800   3580           0.00020014422  0.00013848097       2701 
     36000   3600           0.00020165626  0.00013796434       2701 
     36200   3620           0.00020297057  0.0001346407        2701 
     36400   3640           0.00020432584  0.00012838525       2701 
     36600   3660           0.00020530152  0.00012848442       2701 
     36800   3680           0.00020709012  0.0001296875        2701 
     37000   3700           0.00020939979  0.00017016832       2701 
     37200   3720           0.00021026158  0.00017388254       2701 
     37400   3740           0.00021203076  0.00012169741       2701 
     37600   3760           0.00021407912  0.00012467048       2701 
     37800   3780           0.00021652866  0.000129545         2701 
     38000   3800           0.00021927979  0.00013537464       2701 
     38200   3820           0.00022175274  0.00014124275       2701 
     38400   3840           0.00022431717  0.0001456533        2701 
     38600   3860           0.00022586947  0.00015646735       2701 
     38800   3880           0.00021974508  0.0001467496        2701 
     39000   3900           0.00021270891  0.0001291023        2701 
     39200   3920           0.00020709839  0.00014468038       2701 
     39400   3940           0.00020138943  0.000156103         2701 
     39600   3960           0.00019579027  0.00015207179       2701 
     39800   3980           0.00019219602  0.0001548601        2701 
     40000   4000           0.00018931715  0.00013543387       2701 
Loop time of 169.513 on 4 procs for 40000 steps with 2701 atoms

Performance: 2038784.562 tau/day, 235.970 timesteps/s, 637.356 katom-step/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 16.279     | 22.828     | 28         |  98.9 | 13.47
Bond    | 0.88503    | 1.4645     | 2.0916     |  36.3 |  0.86
Neigh   | 29.832     | 29.954     | 30.069     |   1.5 | 17.67
Comm    | 1.2274     | 1.3406     | 1.4623     |   7.3 |  0.79
Output  | 0.0041506  | 0.0054325  | 0.0062685  |   1.1 |  0.00
Modify  | 107.8      | 113.27     | 120.23     |  47.8 | 66.82
Other   |            | 0.6549     |            |       |  0.39

Nlocal:         675.25 ave        1362 max           1 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:          94.75 ave         154 max          45 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:          10485 ave       21200 max          18 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:      20408.5 ave       41306 max          18 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 81634
Ave neighs/atom = 30.223621
Ave special neighs/atom = 1.7304702
Neighbor list builds = 39994
Dangerous builds = 0
Total wall time: 0:02:50
